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Longin CFH, Reif JC. Redesigning the exploitation of wheat genetic resources. TRENDS IN PLANT SCIENCE 2014; 19:631-6. [PMID: 25052155 DOI: 10.1016/j.tplants.2014.06.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/20/2014] [Accepted: 06/29/2014] [Indexed: 05/19/2023]
Abstract
More than half a million wheat genetic resources are resting in gene banks worldwide. Unlocking their hidden favorable genetic diversity for breeding is pivotal for enhancing grain yield potential, and averting future food shortages. Here, we propose exploiting recent advances in hybrid wheat technology to uncover the masked breeding values of wheat genetic resources. The gathered phenotypic information will enable a targeted choice of accessions with high value for pre-breeding among this plethora of genetic resources. We intend to provoke a paradigm shift in pre-breeding strategies for grain yield, moving away from allele mining toward genome-wide selection to bridge the yield gap between genetic resources and elite breeding pools.
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Affiliation(s)
- C Friedrich H Longin
- State Plant Breeding Institute, University of Hohenheim, 70599 Stuttgart, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany.
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102
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Belova T, Grønvold L, Kumar A, Kianian S, He X, Lillemo M, Springer NM, Lien S, Olsen OA, Sandve SR. Utilization of deletion bins to anchor and order sequences along the wheat 7B chromosome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:2029-2040. [PMID: 25134516 DOI: 10.1007/s00122-014-2358-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 07/13/2014] [Indexed: 06/03/2023]
Abstract
A total of 3,671 sequence contigs and scaffolds were mapped to deletion bins on wheat chromosome 7B providing a foundation for developing high-resolution integrated physical map for this chromosome. Bread wheat (Triticum aestivum L.) has a large, complex and highly repetitive genome which is challenging to assemble into high quality pseudo-chromosomes. As part of the international effort to sequence the hexaploid bread wheat genome by the international wheat genome sequencing consortium (IWGSC) we are focused on assembling a reference sequence for chromosome 7B. The successful completion of the reference chromosome sequence is highly dependent on the integration of genetic and physical maps. To aid the integration of these two types of maps, we have constructed a high-density deletion bin map of chromosome 7B. Using the 270 K Nimblegen comparative genomic hybridization (CGH) array on a set of cv. Chinese spring deletion lines, a total of 3,671 sequence contigs and scaffolds (~7.8 % of chromosome 7B physical length) were mapped into nine deletion bins. Our method of genotyping deletions on chromosome 7B relied on a model-based clustering algorithm (Mclust) to accurately predict the presence or absence of a given genomic sequence in a deletion line. The bin mapping results were validated using three different approaches, viz. (a) PCR-based amplification of randomly selected bin mapped sequences (b) comparison with previously mapped ESTs and (c) comparison with a 7B genetic map developed in the present study. Validation of the bin mapping results suggested a high accuracy of the assignment of 7B sequence contigs and scaffolds to the 7B deletion bins.
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Affiliation(s)
- Tatiana Belova
- Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway,
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103
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Hao M, Luo J, Zeng D, Zhang L, Ning S, Yuan Z, Yan Z, Zhang H, Zheng Y, Feuillet C, Choulet F, Yen Y, Zhang L, Liu D. QTug.sau-3B is a major quantitative trait locus for wheat hexaploidization. G3 (BETHESDA, MD.) 2014; 4:1943-53. [PMID: 25128436 PMCID: PMC4199700 DOI: 10.1534/g3.114.013078] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 08/12/2014] [Indexed: 11/18/2022]
Abstract
Meiotic nonreduction resulting in unreduced gametes is thought to be the predominant mechanism underlying allopolyploid formation in plants. Until now, however, its genetic base was largely unknown. The allohexaploid crop common wheat (Triticum aestivum L.), which originated from hybrids of T. turgidum L. with Aegilops tauschii Cosson, provides a model to address this issue. Our observations of meiosis in pollen mother cells from T. turgidum×Ae. tauschii hybrids indicated that first division restitution, which exhibited prolonged cell division during meiosis I, was responsible for unreduced gamete formation. A major quantitative trait locus (QTL) for this trait, named QTug.sau-3B, was detected on chromosome 3B in two T. turgidum×Ae. tauschii haploid populations. This QTL is situated between markers Xgwm285 and Xcfp1012 and covered a genetic distance of 1 cM in one population. QTug.sau-3B is a haploid-dependent QTL because it was not detected in doubled haploid populations. Comparative genome analysis indicated that this QTL was close to Ttam-3B, a collinear homolog of tam in wheat. Although the relationship between QTug.sau-3B and Ttam requires further study, high frequencies of unreduced gametes may be related to reduced expression of Ttam in wheat.
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Affiliation(s)
- Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, Sichuan 611130, People's Republic of China
| | - Jiangtao Luo
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, Sichuan 611130, People's Republic of China
| | - Deying Zeng
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, Sichuan 611130, People's Republic of China
| | - Li Zhang
- Institute of Ecological Forestry, Sichuan Agricultural University at Chengdu, Wenjiang, Sichuan 611130, People's Republic of China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, Sichuan 611130, People's Republic of China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, Sichuan 611130, People's Republic of China
| | - Zehong Yan
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, Sichuan 611130, People's Republic of China
| | - Huaigang Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, People's Republic of China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, Sichuan 611130, People's Republic of China
| | - Catherine Feuillet
- INRA University Blaise Pascal, Joint Research Unit 1095 Genetics Diversity and Ecophysiology of Cereals, Clermont-Ferrand 63039, France
| | - Frédéric Choulet
- INRA University Blaise Pascal, Joint Research Unit 1095 Genetics Diversity and Ecophysiology of Cereals, Clermont-Ferrand 63039, France
| | - Yang Yen
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota 57007
| | - Lianquan Zhang
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, Sichuan 611130, People's Republic of China
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University at Chengdu, Wenjiang, Sichuan 611130, People's Republic of China Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, People's Republic of China
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104
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Affiliation(s)
- Kellye Eversole
- International Wheat Genome Sequencing Consortium, 5207 Wyoming Road, Bethesda, MD 20816, USA
| | - Catherine Feuillet
- International Wheat Genome Sequencing Consortium, 5207 Wyoming Road, Bethesda, MD 20816, USA. Bayer CropScience, Innovation Center, 3500 Paramount Parkway, Morrisville, NC 27560, USA
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Zentrum Munich, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium, 5207 Wyoming Road, Bethesda, MD 20816, USA
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105
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Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, Leroy P, Mangenot S, Guilhot N, Le Gouis J, Balfourier F, Alaux M, Jamilloux V, Poulain J, Durand C, Bellec A, Gaspin C, Safar J, Dolezel J, Rogers J, Vandepoele K, Aury JM, Mayer K, Berges H, Quesneville H, Wincker P, Feuillet C. Structural and functional partitioning of bread wheat chromosome 3B. Science 2014; 345:1249721. [PMID: 25035497 DOI: 10.1126/science.1249721] [Citation(s) in RCA: 389] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits.
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Affiliation(s)
- Frédéric Choulet
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France.
| | - Adriana Alberti
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Sébastien Theil
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Natasha Glover
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Valérie Barbe
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Josquin Daron
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Lise Pingault
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Pierre Sourdille
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Arnaud Couloux
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Etienne Paux
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Philippe Leroy
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Sophie Mangenot
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Nicolas Guilhot
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Jacques Le Gouis
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Francois Balfourier
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
| | - Michael Alaux
- INRA, UR1164 Unité de Recherche Génomique Info Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, 78026 Versailles, France
| | - Véronique Jamilloux
- INRA, UR1164 Unité de Recherche Génomique Info Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, 78026 Versailles, France
| | - Julie Poulain
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Céline Durand
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Arnaud Bellec
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge, 31326 Castanet-Tolosan, France
| | - Christine Gaspin
- Biométrie et Intelligence Artificielle, INRA, Chemin de Borde Rouge, BP 27, 31326 Castanet-Tolosan, France
| | - Jan Safar
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Jaroslav Dolezel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Slechtitelu 31, CZ-78371 Olomouc, Czech Republic
| | - Jane Rogers
- The Genome Analysis Centre, Norwich, Norwich Research Park, Norwich NR4 7UH, UK
| | - Klaas Vandepoele
- Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics (Ghent University), Technologiepark 927, 9052 Gent, Belgium
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France
| | - Klaus Mayer
- Munich Information Center for Protein Sequences, Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Muenchen, D-85764 Neuherberg, Germany
| | - Hélène Berges
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge, 31326 Castanet-Tolosan, France
| | - Hadi Quesneville
- INRA, UR1164 Unité de Recherche Génomique Info Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, 78026 Versailles, France
| | - Patrick Wincker
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91000 Evry, France. CNRS UMR 8030, 2 Rue Gaston Crémieux, 91000 Evry, France. Université d'Evry, CP5706 Evry, France
| | - Catherine Feuillet
- Institut National de la Recherche Agronomique (INRA) UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France. University Blaise Pascal, UMR1095, Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France
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106
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Wang Z, Cui Y, Chen Y, Zhang D, Liang Y, Zhang D, Wu Q, Xie J, Ouyang S, Li D, Huang Y, Lu P, Wang G, Yu M, Zhou S, Sun Q, Liu Z. Comparative genetic mapping and genomic region collinearity analysis of the powdery mildew resistance gene Pm41. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1741-51. [PMID: 24906815 DOI: 10.1007/s00122-014-2336-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 05/20/2014] [Indexed: 05/09/2023]
Abstract
By applying comparative genomics analyses, a high-density genetic linkage map narrowed the powdery mildew resistance gene Pm41 originating from wild emmer in a sub-centimorgan genetic interval. Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici, results in large yield losses worldwide. A high-density genetic linkage map of the powdery mildew resistance gene Pm41, originating from wild emmer (Triticum turgidum var. dicoccoides) and previously mapped to the distal region of chromosome 3BL bin 0.63-1.00, was constructed using an F5:6 recombinant inbred line population derived from a cross of durum wheat cultivar Langdon and wild emmer accession IW2. By applying comparative genomics analyses, 19 polymorphic sequence-tagged site markers were developed and integrated into the Pm41 genetic linkage map. Ultimately, Pm41 was mapped in a 0.6 cM genetic interval flanked by markers XWGGC1505 and XWGGC1507, which correspond to 11.7, 19.2, and 24.9 kb orthologous genomic regions in Brachypodium, rice, and sorghum, respectively. The XWGGC1506 marker co-segregated with Pm41 and could be served as a starting point for chromosome landing and map-based cloning as well as marker-assisted selection of Pm41. Detailed comparative genomics analysis of the markers flanking the Pm41 locus in wheat and the putative orthologous genes in Brachypodium, rice, and sorghum suggests that the gene order is highly conserved between rice and sorghum. However, intra-chromosome inversions and re-arrangements are evident in the wheat and Brachypodium genomic regions, and gene duplications are also present in the orthologous genomic regions of Pm41 in wheat, indicating that the Brachypodium gene model can provide more useful information for wheat marker development.
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Affiliation(s)
- Zhenzhong Wang
- State Key Laboratory for Agrobiotechnology, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
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107
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Huang WT, Zhang JR, Xie WY, Shi Y, Luo HQ, Li NB. Fuzzy logic sensing of G-quadruplex DNA and its cleavage reagents based on reduced graphene oxide. Biosens Bioelectron 2014; 57:117-24. [DOI: 10.1016/j.bios.2014.01.055] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 01/27/2014] [Accepted: 01/28/2014] [Indexed: 12/11/2022]
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108
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Poursarebani N, Nussbaumer T, Šimková H, Šafář J, Witsenboer H, van Oeveren J, Doležel J, Mayer KFX, Stein N, Schnurbusch T. Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:334-47. [PMID: 24813060 PMCID: PMC4241024 DOI: 10.1111/tpj.12550] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/25/2014] [Accepted: 05/01/2014] [Indexed: 05/08/2023]
Abstract
Bread wheat (Triticum aestivum L.) is the most important staple food crop for 35% of the world's population. International efforts are underway to facilitate an increase in wheat production, of which the International Wheat Genome Sequencing Consortium (IWGSC) plays an important role. As part of this effort, we have developed a sequence-based physical map of wheat chromosome 6A using whole-genome profiling (WGP™). The bacterial artificial chromosome (BAC) contig assembly tools fingerprinted contig (fpc) and linear topological contig (ltc) were used and their contig assemblies were compared. A detailed investigation of the contigs structure revealed that ltc created a highly robust assembly compared with those formed by fpc. The ltc assemblies contained 1217 contigs for the short arm and 1113 contigs for the long arm, with an L50 of 1 Mb. To facilitate in silico anchoring, WGP™ tags underlying BAC contigs were extended by wheat and wheat progenitor genome sequence information. Sequence data were used for in silico anchoring against genetic markers with known sequences, of which almost 79% of the physical map could be anchored. Moreover, the assigned sequence information led to the 'decoration' of the respective physical map with 3359 anchored genes. Thus, this robust and genetically anchored physical map will serve as a framework for the sequencing of wheat chromosome 6A, and is of immediate use for map-based isolation of agronomically important genes/quantitative trait loci located on this chromosome.
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Affiliation(s)
- Naser Poursarebani
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
- * For correspondence (e-mails and )
| | - Thomas Nussbaumer
- MIPS/IBIS German Research Center for Environmental HealthD-85764, Neuherberg, Germany
- † These authors contributed equally to this work
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchCZ-78371, Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchCZ-78371, Olomouc, Czech Republic
| | | | - Jan van Oeveren
- Keygene N.V.Agro Business Park 90, 6708 PW, Wageningen, The Netherlands
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchCZ-78371, Olomouc, Czech Republic
| | - Klaus FX Mayer
- MIPS/IBIS German Research Center for Environmental HealthD-85764, Neuherberg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
- * For correspondence (e-mails and )
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109
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Bansal U, Bariana H, Wong D, Randhawa M, Wicker T, Hayden M, Keller B. Molecular mapping of an adult plant stem rust resistance gene Sr56 in winter wheat cultivar Arina. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1441-8. [PMID: 24794977 DOI: 10.1007/s00122-014-2311-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 04/10/2014] [Indexed: 05/08/2023]
Abstract
This article covers detailed characterization and naming of QSr.sun - 5BL as Sr56 . Molecular markers linked with adult plant stem rust resistance gene Sr56 were identified and validated for marker-assisted selection. The identification of new sources of adult plant resistance (APR) and effective combinations of major and minor genes is well appreciated in breeding for durable rust resistance in wheat. A QTL, QSr.sun-5BL, contributed by winter wheat cultivar Arina providing 12-15 % reduction in stem rust severity, was reported in an Arina/Forno recombinant inbred line (RIL) population. Following the demonstration of monogenic segregation for APR in the Arina/Yitpi RIL population, the resistance locus was formally named Sr56. Saturation mapping of the Sr56 region using STS (from EST and DArT clones), SNP (9 K) and SSR markers from wheat chromosome survey sequences that were ordered based on synteny with Brachypodium distachyon genes in chromosome 1 resulted in the flanking of Sr56 by sun209 (SSR) and sun320 (STS) at 2.6 and 1.2 cM on the proximal and distal ends, respectively. Investigation of conservation of gene order between the Sr56 region in wheat and B. distachyon showed that the syntenic region defined by SSR marker interval sun209-sun215 corresponded to approximately 192 kb in B. distachyon, which contains five predicted genes. Conservation of gene order for the Sr56 region between wheat and Brachypodium, except for two inversions, provides a starting point for future map-based cloning of Sr56. The Arina/Forno RILs carrying both Sr56 and Sr57 exhibited low disease severity compared to those RILs carrying these genes singly. Markers linked with Sr56 would be useful for marker-assisted pyramiding of this gene with other major and APR genes for which closely linked markers are available.
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Affiliation(s)
- Urmil Bansal
- University of Sydney Plant Breeding Institute-Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia,
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110
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Camilios-Neto D, Bonato P, Wassem R, Tadra-Sfeir MZ, Brusamarello-Santos LCC, Valdameri G, Donatti L, Faoro H, Weiss VA, Chubatsu LS, Pedrosa FO, Souza EM. Dual RNA-seq transcriptional analysis of wheat roots colonized by Azospirillum brasilense reveals up-regulation of nutrient acquisition and cell cycle genes. BMC Genomics 2014; 15:378. [PMID: 24886190 PMCID: PMC4042000 DOI: 10.1186/1471-2164-15-378] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 05/02/2014] [Indexed: 12/20/2022] Open
Abstract
Background The rapid growth of the world’s population demands an increase in food production that no longer can be reached by increasing amounts of nitrogenous fertilizers. Plant growth promoting bacteria (PGPB) might be an alternative to increase nitrogenous use efficiency (NUE) in important crops such wheat. Azospirillum brasilense is one of the most promising PGPB and wheat roots colonized by A. brasilense is a good model to investigate the molecular basis of plant-PGPB interaction including improvement in plant-NUE promoted by PGPB. Results We performed a dual RNA-Seq transcriptional profiling of wheat roots colonized by A. brasilense strain FP2. cDNA libraries from biological replicates of colonized and non-inoculated wheat roots were sequenced and mapped to wheat and A. brasilense reference sequences. The unmapped reads were assembled de novo. Overall, we identified 23,215 wheat expressed ESTs and 702 A. brasilense expressed transcripts. Bacterial colonization caused changes in the expression of 776 wheat ESTs belonging to various functional categories, ranging from transport activity to biological regulation as well as defense mechanism, production of phytohormones and phytochemicals. In addition, genes encoding proteins related to bacterial chemotaxi, biofilm formation and nitrogen fixation were highly expressed in the sub-set of A. brasilense expressed genes. Conclusions PGPB colonization enhanced the expression of plant genes related to nutrient up-take, nitrogen assimilation, DNA replication and regulation of cell division, which is consistent with a higher proportion of colonized root cells in the S-phase. Our data support the use of PGPB as an alternative to improve nutrient acquisition in important crops such as wheat, enhancing plant productivity and sustainability. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-378) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Emanuel M Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR 81531-990, Brazil.
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Diéguez MJ, Pergolesi MF, Velasquez SM, Ingala L, López M, Darino M, Paux E, Feuillet C, Sacco F. Fine mapping of LrSV2, a race-specific adult plant leaf rust resistance gene on wheat chromosome 3BS. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1133-1141. [PMID: 24553966 DOI: 10.1007/s00122-014-2285-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 02/04/2014] [Indexed: 06/03/2023]
Abstract
Fine mapping permits the precise positioning of genes within chromosomes, prerequisite for positional cloning that will allow its rational use and the study of the underlying molecular action mechanism. Three leaf rust resistance genes were identified in the durable leaf rust resistant Argentinean wheat variety Sinvalocho MA: the seedling resistance gene Lr3 on distal 6BL and two adult plant resistance genes, LrSV1 and LrSV2, on chromosomes 2DS and 3BS, respectively. To develop a high-resolution genetic map for LrSV2, 10 markers were genotyped on 343 F2 individuals from a cross between Sinvalocho MA and Gama6. The closest co-dominant markers on both sides of the gene (3 microsatellites and 2 STMs) were analyzed on 965 additional F2s from the same cross. Microsatellite marker cfb5010 cosegregated with LrSV2 whereas flanking markers were found at 1 cM distal and at 0.3 cM proximal to the gene. SSR markers designed from the sequences of cv Chinese Spring BAC clones spanning the LrSV2 genetic interval were tested on the recombinants, allowing the identification of microsatellite swm13 at 0.15 cM distal to LrSV2. This delimited an interval of 0.45 cM around the gene flanked by the SSR markers swm13 and gwm533 at the subtelomeric end of chromosome 3BS.
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Affiliation(s)
- M J Diéguez
- Instituto de Genética "Ewald A. Favret" CICVyA-INTA CC25 (1712) Castelar, Buenos Aires, Argentina,
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Zhang J, Shao C, Zhang L, Liu K, Gao F, Dong Z, Xu P, Chen S. A first generation BAC-based physical map of the half-smooth tongue sole (Cynoglossus semilaevis) genome. BMC Genomics 2014; 15:215. [PMID: 24650389 PMCID: PMC3998196 DOI: 10.1186/1471-2164-15-215] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 03/10/2014] [Indexed: 02/06/2023] Open
Abstract
Background Half-smooth tongue sole (Cynoglossus semilaevis Günther) has been exploited as a commercially important cultured marine flatfish, and female grows 2–3 times faster than male. Genetic studies, especially on the chromosomal sex-determining system of this species, have been carried out in the last decade. Although the genome of half-smooth tongue sole was relatively small (626.9 Mb), there are still some difficulties in the high-quality assembly of the next generation genome sequencing reads without the assistance of a physical map, especially for the W chromosome of this fish due to abundance of repetitive sequences. The objective of this study is to construct a bacterial artificial chromosome (BAC)-based physical map for half-smooth tongue sole with the method of high information content fingerprinting (HICF). Results A physical map of half-smooth tongue sole was constructed with 30, 294 valid fingerprints (7.5 × genome coverage) with a tolerance of 4 and an initial cutoff of 1e-60. A total of 29,709 clones were assembled into 1,485 contigs with an average length of 539 kb and a N50 length of 664 kb. There were 394 contigs longer than the N50 length, and these contigs will be a useful resource for future integration with linkage map and whole genome sequence assembly. The estimated physical length of the assembled contigs was 797 Mb, representing approximately 1.27 coverage of the half-smooth tongue sole genome. The largest contig contained 410 BAC clones with a physical length of 3.48 Mb. Almost all of the 676 BAC clones (99.9%) in the 21 randomly selected contigs were positively validated by PCR assays, thereby confirming the reliability of the assembly. Conclusions A first generation BAC-based physical map of half-smooth tongue sole was constructed with high reliability. The map will promote genetic improvement programs of this fish, especially integration of physical and genetic maps, fine-mappings of important gene and/or QTL, comparative and evolutionary genomics studies, as well as whole genome sequence assembly.
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Affiliation(s)
| | | | | | | | | | | | - Peng Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China.
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113
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Shatalina M, Messmer M, Feuillet C, Mascher F, Paux E, Choulet F, Wicker T, Keller B. High-resolution analysis of a QTL for resistance to Stagonospora nodorum glume blotch in wheat reveals presence of two distinct resistance loci in the target interval. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:573-586. [PMID: 24306318 DOI: 10.1007/s00122-013-2240-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 11/19/2013] [Indexed: 06/02/2023]
Abstract
Stagonospora nodorum glume blotch (SNG), caused by the necrotrophic fungus Stagonospora nodorum, is one of the economically important diseases of bread wheat (Triticum aestivum L.). Resistance to SNG is known to be quantitative and previous studies of a recombinant inbred line (RIL) population identified a major quantitative trait locus (QTL) for resistance to SNG on the short arm of chromosome 3B. To localize this QTL (QSng.sfr-3BS) with high resolution, we constructed a genetic map for the QTL target region using information from sequenced flow-sorted chromosomes 3B of the two parental cultivars 'Arina' and 'Forno', the physical map of chromosome 3B of cultivar 'Chinese Spring' and BAC-clone sequences. The mapping population of near-isogenic lines (NIL) was evaluated for SNG resistance in field infection tests. NILs segregated for disease resistance as well as for plant height; additionally, we observed a high environmental influence on the trait. Our analysis detected a strong negative correlation of SNG resistance and plant height. Further analysis of the target region identified two linked loci associated with SNG resistance. One of them was also associated with plant height, revealing an effect of QSng.sfr-3BS on plant height that was hidden in the RIL population. This result demonstrates an unexpectedly high genetic complexity of resistance controlled by QSng.sfr-3BS and shows the importance of the study of QTL in mendelized form in NILs.
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Affiliation(s)
- Margarita Shatalina
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
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Borrill P, Connorton JM, Balk J, Miller AJ, Sanders D, Uauy C. Biofortification of wheat grain with iron and zinc: integrating novel genomic resources and knowledge from model crops. FRONTIERS IN PLANT SCIENCE 2014; 5:53. [PMID: 24600464 PMCID: PMC3930855 DOI: 10.3389/fpls.2014.00053] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 02/04/2014] [Indexed: 05/18/2023]
Abstract
Wheat, like many other staple cereals, contains low levels of the essential micronutrients iron and zinc. Up to two billion people worldwide suffer from iron and zinc deficiencies, particularly in regions with predominantly cereal-based diets. Although wheat flour is commonly fortified during processing, an attractive and more sustainable solution is biofortification, which requires developing new varieties of wheat with inherently higher iron and zinc content in their grains. Until now most studies aimed at increasing iron and zinc content in wheat grains have focused on discovering natural variation in progenitor or related species. However, recent developments in genomics and transformation have led to a step change in targeted research on wheat at a molecular level. We discuss promising approaches to improve iron and zinc content in wheat using knowledge gained in model grasses. We explore how the latest resources developed in wheat, including sequenced genomes and mutant populations, can be exploited for biofortification. We also highlight the key research and practical challenges that remain in improving iron and zinc content in wheat.
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Affiliation(s)
| | | | - Janneke Balk
- John Innes CentreNorwich, UK
- School of Biological Sciences, University of East AngliaNorwich, UK
| | | | | | - Cristobal Uauy
- John Innes CentreNorwich, UK
- National Institute of Agricultural BotanyCambridge, UK
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Ariyadasa R, Mascher M, Nussbaumer T, Schulte D, Frenkel Z, Poursarebani N, Zhou R, Steuernagel B, Gundlach H, Taudien S, Felder M, Platzer M, Himmelbach A, Schmutzer T, Hedley PE, Muehlbauer GJ, Scholz U, Korol A, Mayer KF, Waugh R, Langridge P, Graner A, Stein N. A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms. PLANT PHYSIOLOGY 2014; 164:412-23. [PMID: 24243933 PMCID: PMC3875818 DOI: 10.1104/pp.113.228213] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 11/13/2013] [Indexed: 05/18/2023]
Abstract
Barley (Hordeum vulgare) is an important cereal crop and a model species for Triticeae genomics. To lay the foundation for hierarchical map-based sequencing, a genome-wide physical map of its large and complex 5.1 billion-bp genome was constructed by high-information content fingerprinting of almost 600,000 bacterial artificial chromosomes representing 14-fold haploid genome coverage. The resultant physical map comprises 9,265 contigs with a cumulative size of 4.9 Gb representing 96% of the physical length of the barley genome. The reliability of the map was verified through extensive genetic marker information and the analysis of topological networks of clone overlaps. A minimum tiling path of 66,772 minimally overlapping clones was defined that will serve as a template for hierarchical clone-by-clone map-based shotgun sequencing. We integrated whole-genome shotgun sequence data from the individuals of two mapping populations with published bacterial artificial chromosome survey sequence information to genetically anchor the physical map. This novel approach in combination with the comprehensive whole-genome shotgun sequence data sets allowed us to independently validate and improve a previously reported physical and genetic framework. The resources developed in this study will underpin fine-mapping and cloning of agronomically important genes and the assembly of a draft genome sequence.
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116
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Doležel J, Vrána J, Cápal P, Kubaláková M, Burešová V, Šimková H. Advances in plant chromosome genomics. Biotechnol Adv 2014; 32:122-36. [DOI: 10.1016/j.biotechadv.2013.12.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 12/20/2013] [Accepted: 12/21/2013] [Indexed: 01/09/2023]
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Raats D, Frenkel Z, Krugman T, Dodek I, Sela H, Simková H, Magni F, Cattonaro F, Vautrin S, Bergès H, Wicker T, Keller B, Leroy P, Philippe R, Paux E, Doležel J, Feuillet C, Korol A, Fahima T. The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution. Genome Biol 2013; 14:R138. [PMID: 24359668 PMCID: PMC4053865 DOI: 10.1186/gb-2013-14-12-r138] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 12/20/2013] [Indexed: 11/16/2022] Open
Abstract
Background The wheat genome sequence is an essential tool for advanced genomic research and improvements. The generation of a high-quality wheat genome sequence is challenging due to its complex 17 Gb polyploid genome. To overcome these difficulties, sequencing through the construction of BAC-based physical maps of individual chromosomes is employed by the wheat genomics community. Here, we present the construction of the first comprehensive physical map of chromosome 1BS, and illustrate its unique gene space organization and evolution. Results Fingerprinted BAC clones were assembled into 57 long scaffolds, anchored and ordered with 2,438 markers, covering 83% of chromosome 1BS. The BAC-based chromosome 1BS physical map and gene order of the orthologous regions of model grass species were consistent, providing strong support for the reliability of the chromosome 1BS assembly. The gene space for chromosome 1BS spans the entire length of the chromosome arm, with 76% of the genes organized in small gene islands, accompanied by a two-fold increase in gene density from the centromere to the telomere. Conclusions This study provides new evidence on common and chromosome-specific features in the organization and evolution of the wheat genome, including a non-uniform distribution of gene density along the centromere-telomere axis, abundance of non-syntenic genes, the degree of colinearity with other grass genomes and a non-uniform size expansion along the centromere-telomere axis compared with other model cereal genomes. The high-quality physical map constructed in this study provides a solid basis for the assembly of a reference sequence of chromosome 1BS and for breeding applications.
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118
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Salentijn EM, Esselink DG, Goryunova SV, van der Meer IM, Gilissen LJWJ, Smulders MJM. Quantitative and qualitative differences in celiac disease epitopes among durum wheat varieties identified through deep RNA-amplicon sequencing. BMC Genomics 2013; 14:905. [PMID: 24354426 PMCID: PMC3890609 DOI: 10.1186/1471-2164-14-905] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 12/10/2013] [Indexed: 12/20/2022] Open
Abstract
Background Wheat gluten is important for the industrial quality of bread wheat (Triticum aestivum L.) and durum wheat (T. turgidum L.). Gluten proteins are also the source of immunogenic peptides that can trigger a T cell reaction in celiac disease (CD) patients, leading to inflammatory responses in the small intestine. Various peptides with three major T cell epitopes involved in CD are derived from alpha-gliadin fraction of gluten. Alpha-gliadins are encoded by a large multigene family and amino acid variation in the CD epitopes is known to influence the immunogenicity of individual gene family members. Current commercial methods of gluten detection are unable to distinguish between immunogenic and non-immunogenic CD epitope variants and thus to accurately quantify the overall CD epitope load of a given wheat variety. Such quantification is indispensable for correct selection of wheat varieties with low potential to cause CD. Results A 454 RNA-amplicon sequencing method was developed for alpha-gliadin transcripts encompassing the three major CD epitopes and their variants. The method was used to screen developing grains on plants of 61 different durum wheat cultivars and accessions. A dedicated sequence analysis pipeline returned a total of 304 unique alpha-gliadin transcripts, corresponding to a total of 171 ‘unique deduced protein fragments’ of alpha-gliadins. The numbers of these fragments obtained in each plant were used to calculate quantitative and quantitative differences between the CD epitopes expressed in the endosperm of these wheat plants. A few plants showed a lower fraction of CD epitope-encoding alpha-gliadin transcripts, but none were free of CD epitopes. Conclusions The dedicated 454 RNA-amplicon sequencing method enables 1) the grouping of wheat plants according to the genetic variation in alpha-gliadin transcripts, and 2) the screening for plants which are potentially less CD-immunogenic. The resulting alpha-gliadin sequence database will be useful as a reference in proteomics analysis regarding the immunogenic potential of mature wheat grains.
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Affiliation(s)
- Elma Mj Salentijn
- Plant Research International, Wageningen UR, P,O, Box 16, Wageningen, AA NL-6700, The Netherlands.
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Evaluation of assembly strategies using RNA-seq data associated with grain development of wheat (Triticum aestivum L.). PLoS One 2013; 8:e83530. [PMID: 24349528 PMCID: PMC3861526 DOI: 10.1371/journal.pone.0083530] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 11/05/2013] [Indexed: 11/19/2022] Open
Abstract
Wheat (Triticum aestivum L.) is one of the most important crops cultivated worldwide. Identifying the complete transcriptome of wheat grain could serve as foundation for further study of wheat seed development. However, the relatively large size and the polyploid complexity of the genome have been substantial barriers to molecular genetics and transcriptome analysis of wheat. Alternatively, RNA sequencing has provided some useful information about wheat genes. However, because of the large number of short reads generated by RNA sequencing, factors that are crucial to transcriptome assembly, including software, candidate parameters and assembly strategies, need to be optimized and evaluated for wheat data. In the present study, four cDNA libraries associated with wheat grain development were constructed and sequenced. A total of 14.17 Gb of high-quality reads were obtained and used to assess different assembly strategies. The most successful approach was to filter the reads with Q30 prior to de novo assembly using Trinity, merge the assembled contigs with genes available in wheat cDNA reference data sets, and combine the resulting assembly with an assembly from a reference-based strategy. Using this approach, a relatively accurate and nearly complete transcriptome associated with wheat grain development was obtained, suggesting that this is an effective strategy for generation of a high-quality transcriptome from RNA sequencing data.
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Timonova EM, Dobrovol’skaya OB, Sergeeva EM, Bildanova LL, Sourdille P, Feuillet C, Salina EA. A comparative genetic and cytogenetic mapping of wheat chromosome 5B using introgression lines. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413120132] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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121
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Mochida K, Shinozaki K. Unlocking Triticeae genomics to sustainably feed the future. PLANT & CELL PHYSIOLOGY 2013; 54:1931-50. [PMID: 24204022 PMCID: PMC3856857 DOI: 10.1093/pcp/pct163] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/04/2013] [Indexed: 05/23/2023]
Abstract
The tribe Triticeae includes the major crops wheat and barley. Within the last few years, the whole genomes of four Triticeae species-barley, wheat, Tausch's goatgrass (Aegilops tauschii) and wild einkorn wheat (Triticum urartu)-have been sequenced. The availability of these genomic resources for Triticeae plants and innovative analytical applications using next-generation sequencing technologies are helping to revitalize our approaches in genetic work and to accelerate improvement of the Triticeae crops. Comparative genomics and integration of genomic resources from Triticeae plants and the model grass Brachypodium distachyon are aiding the discovery of new genes and functional analyses of genes in Triticeae crops. Innovative approaches and tools such as analysis of next-generation populations, evolutionary genomics and systems approaches with mathematical modeling are new strategies that will help us discover alleles for adaptive traits to future agronomic environments. In this review, we provide an update on genomic tools for use with Triticeae plants and Brachypodium and describe emerging approaches toward crop improvements in Triticeae.
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Affiliation(s)
- Keiichi Mochida
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 230-0045 Japan
| | - Kazuo Shinozaki
- Biomass Research Platform Team, Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
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122
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Next generation characterisation of cereal genomes for marker discovery. BIOLOGY 2013; 2:1357-77. [PMID: 24833229 PMCID: PMC4009793 DOI: 10.3390/biology2041357] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/29/2013] [Accepted: 11/08/2013] [Indexed: 12/30/2022]
Abstract
Cereal crops form the bulk of the world’s food sources, and thus their importance cannot be understated. Crop breeding programs increasingly rely on high-resolution molecular genetic markers to accelerate the breeding process. The development of these markers is hampered by the complexity of some of the major cereal crop genomes, as well as the time and cost required. In this review, we address current and future methods available for the characterisation of cereal genomes, with an emphasis on faster and more cost effective approaches for genome sequencing and the development of markers for trait association and marker assisted selection (MAS) in crop breeding programs.
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123
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Breen J, Wicker T, Shatalina M, Frenkel Z, Bertin I, Philippe R, Spielmeyer W, Šimková H, Šafář J, Cattonaro F, Scalabrin S, Magni F, Vautrin S, Bergès H, Paux E, Fahima T, Doležel J, Korol A, Feuillet C, Keller B. A physical map of the short arm of wheat chromosome 1A. PLoS One 2013; 8:e80272. [PMID: 24278269 PMCID: PMC3836966 DOI: 10.1371/journal.pone.0080272] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 10/11/2013] [Indexed: 12/31/2022] Open
Abstract
Bread wheat (Triticum aestivum) has a large and highly repetitive genome which poses major technical challenges for its study. To aid map-based cloning and future genome sequencing projects, we constructed a BAC-based physical map of the short arm of wheat chromosome 1A (1AS). From the assembly of 25,918 high information content (HICF) fingerprints from a 1AS-specific BAC library, 715 physical contigs were produced that cover almost 99% of the estimated size of the chromosome arm. The 3,414 BAC clones constituting the minimum tiling path were end-sequenced. Using a gene microarray containing ∼40 K NCBI UniGene EST clusters, PCR marker screening and BAC end sequences, we arranged 160 physical contigs (97 Mb or 35.3% of the chromosome arm) in a virtual order based on synteny with Brachypodium, rice and sorghum. BAC end sequences and information from microarray hybridisation was used to anchor 3.8 Mbp of Illumina sequences from flow-sorted chromosome 1AS to BAC contigs. Comparison of genetic and synteny-based physical maps indicated that ∼50% of all genetic recombination is confined to 14% of the physical length of the chromosome arm in the distal region. The 1AS physical map provides a framework for future genetic mapping projects as well as the basis for complete sequencing of chromosome arm 1AS.
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Affiliation(s)
- James Breen
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | | | - Zeev Frenkel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Isabelle Bertin
- INRA UMR 1095, Genetique Diversite et Ecophysiologie des Cereales, Clermont-Ferrand, France
| | - Romain Philippe
- INRA UMR 1095, Genetique Diversite et Ecophysiologie des Cereales, Clermont-Ferrand, France
| | | | - Hana Šimková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Jan Šafář
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | | | | | | | | | | | | | - Etienne Paux
- INRA UMR 1095, Genetique Diversite et Ecophysiologie des Cereales, Clermont-Ferrand, France
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Jaroslav Doležel
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Catherine Feuillet
- INRA UMR 1095, Genetique Diversite et Ecophysiologie des Cereales, Clermont-Ferrand, France
| | - Beat Keller
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
- * E-mail:
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Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, Schmutz J, Barry K, Muñoz-Amatriaín M, Close TJ, Wise RP, Schulman AH, Himmelbach A, Mayer KFX, Scholz U, Poland JA, Stein N, Waugh R. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:718-27. [PMID: 23998490 PMCID: PMC4298792 DOI: 10.1111/tpj.12319] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/07/2013] [Accepted: 08/29/2013] [Indexed: 05/18/2023]
Abstract
Next-generation whole-genome shotgun assemblies of complex genomes are highly useful, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows de novo production of a genetically anchored linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1 Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to various genetically ordered sequence-based genotypic datasets. The method is independent of the need for any prior sequence resources, and will enable rapid and cost-efficient establishment of powerful genomic information for many species.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)D–06466 Seeland OT, Gatersleben, Germany
- For correspondence (e-mails ; )
| | - Gary J Muehlbauer
- University of Minnesota, Department of Agronomy and Plant GeneticsSt Paul, MN, 55108, USA
- University of Minnesota, Department of Plant BiologySt Paul, MN 55108, USA
- For correspondence (e-mails ; )
| | - Daniel S Rokhsar
- Department of Energy Joint Genome Institute2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- Department of Molecular and Cell Biology, University of CaliforniaBerkeley, CA, 94720, USA
| | - Jarrod Chapman
- Department of Energy Joint Genome Institute2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute of BiotechnologyHuntsville, AL, 35806, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - María Muñoz-Amatriaín
- University of Minnesota, Department of Agronomy and Plant GeneticsSt Paul, MN, 55108, USA
| | - Timothy J Close
- Department of Botany & Plant Sciences, University of CaliforniaRiverside, CA, 92521, USA
| | - Roger P Wise
- US Department of Agriculture/Agricultural Research Service, Department of Plant Pathology & Microbiology, Iowa State UniversityAmes, IA, 50011–1020, USA
| | - Alan H Schulman
- Institute of Biotechnology, University of Helsinki/MTT Agrifood ResearchPO Box 65, 00014, Helsinki, Finland
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)D–06466 Seeland OT, Gatersleben, Germany
| | - Klaus FX Mayer
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum MünchenD–85764, Neuherberg, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)D–06466 Seeland OT, Gatersleben, Germany
| | - Jesse A Poland
- US Department of Agriculture/Agricultural Research Service, Hard Winter Wheat Genetics Research Unit and Department of Agronomy, Kansas State UniversityManhattan, KS, 65506, USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)D–06466 Seeland OT, Gatersleben, Germany
| | - Robbie Waugh
- Division of Plant Sciences, University of Dundee at the James Hutton InstituteInvergowrie, Dundee, DD2 5DA, UK
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Pascovici D, Gardiner DM, Song X, Breen E, Solomon PS, Keighley T, Molloy MP. Coverage and Consistency: Bioinformatics Aspects of the Analysis of Multirun iTRAQ Experiments with Wheat Leaves. J Proteome Res 2013; 12:4870-81. [DOI: 10.1021/pr400531y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Dana Pascovici
- Australian
Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
| | - Donald M. Gardiner
- CSIRO Plant Industry, Queensland Bioscience
Precinct, 306 Carmody Road, Brisbane, QLD 4067, Australia
| | - Xiaomin Song
- Australian
Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
| | - Edmond Breen
- Australian
Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
| | - Peter S. Solomon
- Plant
Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Tim Keighley
- Australian
Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
| | - Mark P. Molloy
- Australian
Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
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126
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Karafiátová M, Bartoš J, Kopecký D, Ma L, Sato K, Houben A, Stein N, Doležel J. Mapping nonrecombining regions in barley using multicolor FISH. Chromosome Res 2013; 21:739-51. [DOI: 10.1007/s10577-013-9380-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 08/26/2013] [Accepted: 08/30/2013] [Indexed: 12/22/2022]
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127
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Steinbach D, Alaux M, Amselem J, Choisne N, Durand S, Flores R, Keliet AO, Kimmel E, Lapalu N, Luyten I, Michotey C, Mohellibi N, Pommier C, Reboux S, Valdenaire D, Verdelet D, Quesneville H. GnpIS: an information system to integrate genetic and genomic data from plants and fungi. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013; 2013:bat058. [PMID: 23959375 PMCID: PMC3746681 DOI: 10.1093/database/bat058] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Data integration is a key challenge for modern bioinformatics. It aims to provide biologists with tools to explore relevant data produced by different studies. Large-scale international projects can generate lots of heterogeneous and unrelated data. The challenge is to integrate this information with other publicly available data. Nucleotide sequencing throughput has been improved with new technologies; this increases the need for powerful information systems able to store, manage and explore data. GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Institute for Agricultural Research. Here, we illustrate its use. Database URL: http://urgi.versailles.inra.fr/gnpis
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Affiliation(s)
- Delphine Steinbach
- INRA, UR1164 URGI - Research Unit in Genomics-Info, INRA de Versailles, Route de Saint-Cyr, Versailles, 78026, France
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128
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Bassi FM, Kumar A, Zhang Q, Paux E, Huttner E, Kilian A, Dizon R, Feuillet C, Xu SS, Kianian SF. Radiation hybrid QTL mapping of Tdes2 involved in the first meiotic division of wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1977-1990. [PMID: 23715938 DOI: 10.1007/s00122-013-2111-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 04/20/2013] [Indexed: 06/02/2023]
Abstract
Since the dawn of wheat cytogenetics, chromosome 3B has been known to harbor a gene(s) that, when removed, causes chromosome desynapsis and gametic sterility. The lack of natural genetic diversity for this gene(s) has prevented any attempt to fine map and further characterize it. Here, gamma radiation treatment was used to create artificial diversity for this locus. A total of 696 radiation hybrid lines were genotyped with a custom mini array of 140 DArT markers, selected to evenly span the whole 3B chromosome. The resulting map spanned 2,852 centi Ray with a calculated resolution of 0.384 Mb. Phenotyping for the occurrence of meiotic desynapsis was conducted by measuring the level of gametic sterility as seeds produced per spikelet and pollen viability at booting. Composite interval mapping revealed a single QTL with LOD of 16.2 and r (2) of 25.6 % between markers wmc326 and wPt-8983 on the long arm of chromosome 3B. By independent analysis, the location of the QTL was confirmed to be within the deletion bin 3BL7-0.63-1.00 and to correspond to a single gene located ~1.4 Mb away from wPt-8983. The meiotic behavior of lines lacking this gene was characterized cytogenetically to reveal striking similarities with mutants for the dy locus, located on the syntenic chromosome 3 of maize. This represents the first example to date of employing radiation hybrids for QTL analysis. The success achieved by this approach provides an ideal starting point for the final cloning of this interesting gene involved in meiosis of cereals.
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Affiliation(s)
- F M Bassi
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA.
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129
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Rustgi S, Shafqat MN, Kumar N, Baenziger PS, Ali ML, Dweikat I, Campbell BT, Gill KS. Genetic dissection of yield and its component traits using high-density composite map of wheat chromosome 3A: bridging gaps between QTLs and underlying genes. PLoS One 2013; 8:e70526. [PMID: 23894667 PMCID: PMC3722237 DOI: 10.1371/journal.pone.0070526] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 06/25/2013] [Indexed: 11/18/2022] Open
Abstract
Earlier we identified wheat (Triticum aestivum L.) chromosome 3A as a major determinant of grain yield and its component traits. In the present study, a high-density genetic linkage map of 81 chromosome 3A-specific markers was developed to increase the precision of previously identified yield component QTLs, and to map QTLs for biomass-related traits. Many of the previously identified QTLs for yield and its component traits were confirmed and were localized to narrower intervals. Four novel QTLs one each for shoot biomass (Xcfa2262-Xbcd366), total biomass (wPt2740-Xcfa2076), kernels/spike (KPS) (Xwmc664-Xbarc67), and Pseudocercosporella induced lodging (PsIL) were also detected. The major QTLs identified for grain yield (GY), KPS, grain volume weight (GVWT) and spikes per square meter (SPSM) respectively explained 23.2%, 24.2%, 20.5% and 20.2% of the phenotypic variation. Comparison of the genetic map with the integrated physical map allowed estimation of recombination frequency in the regions of interest and suggested that QTLs for grain yield detected in the marker intervals Xcdo549-Xbarc310 and Xpsp3047-Xbarc356 reside in the high-recombination regions, thus should be amenable to map-based cloning. On the other hand, QTLs for KPS and SPSM flanked by markers Xwmc664 and Xwmc489 mapped in the low-recombination region thus are not suitable for map-based cloning. Comparisons with the rice (Oryza sativa L.) genomic DNA sequence identified 11 candidate genes (CGs) for yield and yield related QTLs of which chromosomal location of two (CKX2 and GID2-like) was confirmed using wheat aneuploids. This study provides necessary information to perform high-resolution mapping for map-based cloning and for CG-based cloning of yield QTLs.
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Affiliation(s)
- Sachin Rustgi
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Mustafa N. Shafqat
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Neeraj Kumar
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - P. Stephen Baenziger
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - M. Liakat Ali
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Ismail Dweikat
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - B. Todd Campbell
- Agricultural Research Service, Coastal Plains Soil, Water, and Plant Research Center, Florence, South Carolina, United States of America
| | - Kulvinder Singh Gill
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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130
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Abstract
The emergence of new sequencing technologies has provided fast and cost-efficient strategies for high-resolution mapping of complex genomes. Although these approaches hold great promise to accelerate genome analysis, their application in studying genetic variation in wheat has been hindered by the complexity of its polyploid genome. Here, we applied the next-generation sequencing of a wheat doubled-haploid mapping population for high-resolution gene mapping and tested its utility for ordering shotgun sequence contigs of a flow-sorted wheat chromosome. A bioinformatical pipeline was developed for reliable variant analysis of sequence data generated for polyploid wheat mapping populations. The results of variant mapping were consistent with the results obtained using the wheat 9000 SNP iSelect assay. A reference map of the wheat genome integrating 2740 gene-associated single-nucleotide polymorphisms from the wheat iSelect assay, 1351 diversity array technology, 118 simple sequence repeat/sequence-tagged sites, and 416,856 genotyping-by-sequencing markers was developed. By analyzing the sequenced megabase-size regions of the wheat genome we showed that mapped markers are located within 40-100 kb from genes providing a possibility for high-resolution mapping at the level of a single gene. In our population, gene loci controlling a seed color phenotype cosegregated with 2459 markers including one that was located within the red seed color gene. We demonstrate that the high-density reference map presented here is a useful resource for gene mapping and linking physical and genetic maps of the wheat genome.
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131
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Krasileva KV, Buffalo V, Bailey P, Pearce S, Ayling S, Tabbita F, Soria M, Wang S, Akhunov E, Uauy C, Dubcovsky J. Separating homeologs by phasing in the tetraploid wheat transcriptome. Genome Biol 2013; 14:R66. [PMID: 23800085 PMCID: PMC4053977 DOI: 10.1186/gb-2013-14-6-r66] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Accepted: 06/25/2013] [Indexed: 11/10/2022] Open
Abstract
Background The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs. Results A total of 489 million 100 bp paired-end reads from tetraploid wheat assemble in 140,118 contigs, including 96% of the benchmark cDNAs. We used a comparative genomics approach to annotate 66,633 open reading frames. The multiple k-mer assembly strategy increases the proportion of cDNAs assembled full-length in a single contig by 22% relative to the best single k-mer size. Homoeologs are separated using a post-assembly pipeline that includes polymorphism identification, phasing of SNPs, read sorting, and re-assembly of phased reads. Using a reference set of genes, we determine that 98.7% of SNPs analyzed are correctly separated by phasing. Conclusions Our study shows that de novo transcriptome assembly of tetraploid wheat benefit from multiple k-mer assembly strategies more than diploid wheat. Our results also demonstrate that phasing approaches originally designed for heterozygous diploid organisms can be used to separate the close homoeologous genomes of tetraploid wheat. The predicted tetraploid wheat proteome and gene models provide a valuable tool for the wheat research community and for those interested in comparative genomic studies.
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132
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Philippe R, Paux E, Bertin I, Sourdille P, Choulet F, Laugier C, Šimková H, Šafář J, Bellec A, Vautrin S, Frenkel Z, Cattonaro F, Magni F, Scalabrin S, Martis MM, Mayer KFX, Korol A, Bergès H, Doležel J, Feuillet C. A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat. Genome Biol 2013; 14:R64. [PMID: 23800011 PMCID: PMC4054855 DOI: 10.1186/gb-2013-14-6-r64] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 05/24/2013] [Accepted: 06/25/2013] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning. RESULTS Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome. CONCLUSIONS Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing.
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Affiliation(s)
- Romain Philippe
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Etienne Paux
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Isabelle Bertin
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Pierre Sourdille
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Fréderic Choulet
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Christel Laugier
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic
| | - Jan Šafář
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic
| | - Arnaud Bellec
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326 Castalnet Tolosan, France
| | - Sonia Vautrin
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326 Castalnet Tolosan, France
| | - Zeev Frenkel
- University of Haifa, Institute of Evolution and Department of Evolutionary and Environmental Biology, Haifa 31905, Israel
| | - Federica Cattonaro
- Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
| | - Federica Magni
- Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
| | - Simone Scalabrin
- Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
| | | | - Klaus FX Mayer
- MIPS/IBIS; Helmholtz-Zentrum München, 85764 Neuherberg, Germany
| | - Abraham Korol
- University of Haifa, Institute of Evolution and Department of Evolutionary and Environmental Biology, Haifa 31905, Israel
| | - Hélène Bergès
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326 Castalnet Tolosan, France
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic
| | - Catherine Feuillet
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
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133
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Abstract
The sequencing of large and complex genomes of crop species, facilitated by new sequencing technologies and bioinformatic approaches, has provided new opportunities for crop improvement. Current challenges include understanding how genetic variation translates into phenotypic performance in the field.
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Affiliation(s)
- Michael W Bevan
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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134
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Genomics approaches for crop improvement against abiotic stress. ScientificWorldJournal 2013; 2013:361921. [PMID: 23844392 PMCID: PMC3690750 DOI: 10.1155/2013/361921] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 04/22/2013] [Indexed: 12/13/2022] Open
Abstract
As sessile organisms, plants are inevitably exposed to one or a combination of stress factors every now and then throughout their growth and development. Stress responses vary considerably even in the same plant species; stress-susceptible genotypes are at one extreme, and stress-tolerant ones are at the other. Elucidation of the stress responses of crop plants is of extreme relevance, considering the central role of crops in food and biofuel production. Crop improvement has been a traditional issue to increase yields and enhance stress tolerance; however, crop improvement against abiotic stresses has been particularly compelling, given the complex nature of these stresses. As traditional strategies for crop improvement approach their limits, the era of genomics research has arisen with new and promising perspectives in breeding improved varieties against abiotic stresses.
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135
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Li N, Jia J, Xia C, Liu X, Kong X. Characterization and mapping of novel chlorophyll deficient mutant genes in durum wheat. BREEDING SCIENCE 2013; 63:169-75. [PMID: 23853511 PMCID: PMC3688378 DOI: 10.1270/jsbbs.63.169] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 12/06/2012] [Indexed: 05/06/2023]
Abstract
The yellow-green leaf mutant has a non-lethal chlorophyll-deficient mutation that can be exploited in photosynthesis and plant development research. A novel yellow-green mutant derived from Triticum durum var. Cappelli displays a yellow-green leaf color from the seedling stage to the mature stage. Examination of the mutant chloroplasts with transmission electron microscopy revealed that the shape of chloroplast changed, grana stacks in the stroma were highly variable in size and disorganized. The pigment content, including chlorophyll a, chlorophyll b, total chlorophyll and carotene, was decreased in the mutant. In contrast, the chla/chlb ratio of the mutants was increased in comparison with the normal green leaves. We also found a reduction in the photosynthetic rate, fluorescence kinetic parameters and yield-related agronomic traits of the mutant. A genetic analysis revealed that two nuclear recessive genes controlled the expression of this trait. The genes were designated ygld1 and ygld2. Two molecular markers co-segregated with these genes. ygld 1 co-segregated with the SSR marker wmc110 on chromosome 5AL and ygld 2 co-segregated with the SSR marker wmc28 on chromosome 5BL. These results will contribute to the gene cloning and the understanding of the mechanisms underlying chlorophyll metabolism and chloroplast development in wheat.
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Affiliation(s)
| | | | | | - Xu Liu
- Corresponding author (e-mail: )
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136
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Wang ZN, Banik M, Cloutier S. Divergent evolutionary mechanisms of co-located Tak/Lrk and Glu-D3 loci revealed by comparative analysis of grass genomes. Genome 2013; 56:195-204. [PMID: 23706072 DOI: 10.1139/gen-2012-0172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Seed storage and disease resistance proteins are major traits of wheat. The study of their gene organization and evolution has some implications in breeding. In this study, we characterized the hexaploid wheat D-genome BAC clone TaBAC703A9 that contains a low molecular weight glutenin locus (Glu-D3) and a resistance gene analogue cluster. With a gene density of one gene per 4.8 kb, the cluster contains four resistance gene analogues, namely Tak703-1, Lrr703, Tak703, and Lrk703. This structural cluster unit was conserved across nine grass genomes, but divergent evolutionary mechanisms have been involved in shaping the Tak/Lrk loci in the different species. Gene duplication was the major force for the Tak/Lrk evolution in oats, maize, barley, wheat, sorghum, and Brachypodium, while tandem duplication drove the expansion of this locus in japonica rice. Despite the close proximity of the Glu-D3 and the Tak/Lrk loci in wheat, the evolutionary mechanisms that drove their amplification differ. The Glu-D3 region had a lower gene density, and its amplification was driven by retroelements.
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Affiliation(s)
- Zi-Ning Wang
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg MB R3T 2M9, Canada
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137
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A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proc Natl Acad Sci U S A 2013; 110:7940-5. [PMID: 23610408 DOI: 10.1073/pnas.1219082110] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The current limitations in genome sequencing technology require the construction of physical maps for high-quality draft sequences of large plant genomes, such as that of Aegilops tauschii, the wheat D-genome progenitor. To construct a physical map of the Ae. tauschii genome, we fingerprinted 461,706 bacterial artificial chromosome clones, assembled contigs, designed a 10K Ae. tauschii Infinium SNP array, constructed a 7,185-marker genetic map, and anchored on the map contigs totaling 4.03 Gb. Using whole genome shotgun reads, we extended the SNP marker sequences and found 17,093 genes and gene fragments. We showed that collinearity of the Ae. tauschii genes with Brachypodium distachyon, rice, and sorghum decreased with phylogenetic distance and that structural genome evolution rates have been high across all investigated lineages in subfamily Pooideae, including that of Brachypodieae. We obtained additional information about the evolution of the seven Triticeae chromosomes from 12 ancestral chromosomes and uncovered a pattern of centromere inactivation accompanying nested chromosome insertions in grasses. We showed that the density of noncollinear genes along the Ae. tauschii chromosomes positively correlates with recombination rates, suggested a cause, and showed that new genes, exemplified by disease resistance genes, are preferentially located in high-recombination chromosome regions.
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138
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Physical mapping integrated with syntenic analysis to characterize the gene space of the long arm of wheat chromosome 1A. PLoS One 2013; 8:e59542. [PMID: 23613713 PMCID: PMC3628912 DOI: 10.1371/journal.pone.0059542] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/15/2013] [Indexed: 12/02/2022] Open
Abstract
Background Bread wheat (Triticum aestivum L.) is one of the most important crops worldwide and its production faces pressing challenges, the solution of which demands genome information. However, the large, highly repetitive hexaploid wheat genome has been considered intractable to standard sequencing approaches. Therefore the International Wheat Genome Sequencing Consortium (IWGSC) proposes to map and sequence the genome on a chromosome-by-chromosome basis. Methodology/Principal Findings We have constructed a physical map of the long arm of bread wheat chromosome 1A using chromosome-specific BAC libraries by High Information Content Fingerprinting (HICF). Two alternative methods (FPC and LTC) were used to assemble the fingerprints into a high-resolution physical map of the chromosome arm. A total of 365 molecular markers were added to the map, in addition to 1122 putative unique transcripts that were identified by microarray hybridization. The final map consists of 1180 FPC-based or 583 LTC-based contigs. Conclusions/Significance The physical map presented here marks an important step forward in mapping of hexaploid bread wheat. The map is orders of magnitude more detailed than previously available maps of this chromosome, and the assignment of over a thousand putative expressed gene sequences to specific map locations will greatly assist future functional studies. This map will be an essential tool for future sequencing of and positional cloning within chromosome 1A.
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139
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Belova T, Zhan B, Wright J, Caccamo M, Asp T, Simková H, Kent M, Bendixen C, Panitz F, Lien S, Doležel J, Olsen OA, Sandve SR. Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat. BMC Genomics 2013; 14:222. [PMID: 23557231 PMCID: PMC3622640 DOI: 10.1186/1471-2164-14-222] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 03/22/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The assembly of the bread wheat genome sequence is challenging due to allohexaploidy and extreme repeat content (>80%). Isolation of single chromosome arms by flow sorting can be used to overcome the polyploidy problem, but the repeat content cause extreme assembly fragmentation even at a single chromosome level. Long jump paired sequencing data (mate pairs) can help reduce assembly fragmentation by joining multiple contigs into single scaffolds. The aim of this work was to assess how mate pair data generated from multiple displacement amplified DNA of flow-sorted chromosomes affect assembly fragmentation of shotgun assemblies of the wheat chromosomes. RESULTS Three mate pair (MP) libraries (2 Kb, 3 Kb, and 5 Kb) were sequenced to a total coverage of 89x and 64x for the short and long arm of chromosome 7B, respectively. Scaffolding using SSPACE improved the 7B assembly contiguity and decreased gene space fragmentation, but the degree of improvement was greatly affected by scaffolding stringency applied. At the lowest stringency the assembly N50 increased by ~7 fold, while at the highest stringency N50 was only increased by ~1.5 fold. Furthermore, a strong positive correlation between estimated scaffold reliability and scaffold assembly stringency was observed. A 7BS scaffold assembly with reduced MP coverage proved that assembly contiguity was affected only to a small degree down to ~50% of the original coverage. CONCLUSION The effect of MP data integration into pair end shotgun assemblies of wheat chromosome was moderate; possibly due to poor contig assembly contiguity, the extreme repeat content of wheat, and the use of amplified chromosomal DNA for MP library construction.
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Affiliation(s)
- Tatiana Belova
- Department of Plant and Environmental Sciences, University of Life Sciences, Ås, Norway
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140
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Terracciano I, Maccaferri M, Bassi F, Mantovani P, Sanguineti MC, Salvi S, Simková H, Doležel J, Massi A, Ammar K, Kolmer J, Tuberosa R. Development of COS-SNP and HRM markers for high-throughput and reliable haplotype-based detection of Lr14a in durum wheat (Triticum durum Desf.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1077-101. [PMID: 23292293 DOI: 10.1007/s00122-012-2038-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 12/17/2012] [Indexed: 05/09/2023]
Abstract
Leaf rust (Puccinia triticina Eriks. & Henn.) is a major disease affecting durum wheat production. The Lr14a-resistant gene present in the durum wheat cv. Creso and its derivative cv. Colosseo is one of the best characterized leaf-rust resistance sources deployed in durum wheat breeding. Lr14a has been mapped close to the simple sequence repeat markers gwm146, gwm344 and wmc10 in the distal portion of the chromosome arm 7BL, a gene-dense region. The objectives of this study were: (1) to enrich the Lr14a region with single nucleotide polymorphisms (SNPs) and high-resolution melting (HRM)-based markers developed from conserved ortholog set (COS) genes and from sequenced Diversity Array Technology (DArT(®)) markers; (2) to further investigate the gene content and colinearity of this region with the Brachypodium and rice genomes. Ten new COS-SNP and five HRM markers were mapped within an 8.0 cM interval spanning Lr14a. Two HRM markers pinpointed the locus in an interval of <1.0 cM and eight COS-SNPs were mapped 2.1-4.1 cM distal to Lr14a. Each marker was tested for its capacity to predict the state of Lr14a alleles (in particular, Lr14-Creso associated to resistance) in a panel of durum wheat elite germplasm including 164 accessions. Two of the most informative markers were converted into KASPar(®) markers. Single assay markers ubw14 and wPt-4038-HRM designed for agarose gel electrophoresis/KASPar(®) assays and high-resolution melting analysis, respectively, as well as the double-marker combinations ubw14/ubw18, ubw14/ubw35 and wPt-4038-HRM-ubw35 will be useful for germplasm haplotyping and for molecular-assisted breeding.
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Affiliation(s)
- Irma Terracciano
- Department of Agricultural Sciences (DipSA), University of Bologna, Viale Fanin 44, Bologna 40127, Italy
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141
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Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 2013; 496:87-90. [PMID: 23535596 DOI: 10.1038/nature11997] [Citation(s) in RCA: 478] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Accepted: 02/08/2013] [Indexed: 01/20/2023]
Abstract
Bread wheat (Triticum aestivum, AABBDD) is one of the most widely cultivated and consumed food crops in the world. However, the complex polyploid nature of its genome makes genetic and functional analyses extremely challenging. The A genome, as a basic genome of bread wheat and other polyploid wheats, for example, T. turgidum (AABB), T. timopheevii (AAGG) and T. zhukovskyi (AAGGA(m)A(m)), is central to wheat evolution, domestication and genetic improvement. The progenitor species of the A genome is the diploid wild einkorn wheat T. urartu, which resembles cultivated wheat more extensively than do Aegilops speltoides (the ancestor of the B genome) and Ae. tauschii (the donor of the D genome), especially in the morphology and development of spike and seed. Here we present the generation, assembly and analysis of a whole-genome shotgun draft sequence of the T. urartu genome. We identified protein-coding gene models, performed genome structure analyses and assessed its utility for analysing agronomically important genes and for developing molecular markers. Our T. urartu genome assembly provides a diploid reference for analysis of polyploid wheat genomes and is a valuable resource for the genetic improvement of wheat.
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142
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Alnemer LM, Seetan RI, Bassi FM, Chitraranjan C, Helsene A, Loree P, Goshn SB, Gu YQ, Luo MC, Iqbal MJ, Lazo GR, Denton AM, Kianian SF. Wheat Zapper: a flexible online tool for colinearity studies in grass genomes. Funct Integr Genomics 2013; 13:11-7. [PMID: 23474942 DOI: 10.1007/s10142-013-0317-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 02/08/2013] [Accepted: 02/12/2013] [Indexed: 10/27/2022]
Abstract
In the course of evolution, the genomes of grasses have maintained an observable degree of gene order conservation. The information available for already sequenced genomes can be used to predict the gene order of nonsequenced species by means of comparative colinearity studies. The "Wheat Zapper" application presented here performs on-demand colinearity analysis between wheat, rice, Sorghum, and Brachypodium in a simple, time efficient, and flexible manner. This application was specifically designed to provide plant scientists with a set of tools, comprising not only synteny inference, but also automated primer design, intron/exon boundaries prediction, visual representation using the graphic tool Circos 0.53, and the possibility of downloading FASTA sequences for downstream applications. Quality of the "Wheat Zapper" prediction was confirmed against the genome of maize, with good correlation (r > 0.83) observed between the gene order predicted on the basis of synteny and their actual position on the genome. Further, the accuracy of "Wheat Zapper" was calculated at 0.65 considering the "Genome Zipper" application as the "gold" standard. The differences between these two tools are amply discussed, making the point that "Wheat Zapper" is an accurate and reliable on-demand tool that is sure to benefit the cereal scientific community. The Wheat Zapper is available at http://wge.ndsu.nodak.edu/wheatzapper/ .
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Affiliation(s)
- Loai M Alnemer
- Computer Information Systems Department, The University of Jordan, Amman, 11942, Jordan
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143
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Zhang K, Wang J, Zhang L, Rong C, Zhao F, Peng T, Li H, Cheng D, Liu X, Qin H, Zhang A, Tong Y, Wang D. Association analysis of genomic loci important for grain weight control in elite common wheat varieties cultivated with variable water and fertiliser supply. PLoS One 2013; 8:e57853. [PMID: 23469248 PMCID: PMC3587626 DOI: 10.1371/journal.pone.0057853] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 01/27/2013] [Indexed: 11/18/2022] Open
Abstract
Grain weight, an essential yield component, is under strong genetic control and markedly influenced by the environment. Here, by genome-wide association analysis with a panel of 94 elite common wheat varieties, 37 loci were found significantly associated with thousand-grain weight (TGW) in one or more environments differing in water and fertiliser levels. Five loci were stably associated with TGW under all 12 environments examined. Their elite alleles had positive effects on TGW. Four, two, three, and two loci were consistently associated with TGW in the irrigated and fertilised (IF), rainfed (RF), reduced nitrogen (RN), and reduced phosphorus (RP) environments. The elite alleles of the IF-specific loci enhanced TGW under well-resourced conditions, whereas those of the RF-, RN-, or RP-specific loci conferred tolerance to the TGW decrease when irrigation, nitrogen, or phosphorus were reduced. Moreover, the elite alleles of the environment-independent and -specific loci often acted additively to enhance TGW. Four additional loci were found associated with TGW in specific locations, one of which was shown to contribute to the TGW difference between two experimental sites. Further analysis of 14 associated loci revealed that nine affected both grain length and width, whereas the remaining loci influenced either grain length or width, indicating that these loci control grain weight by regulating kernel size. Finally, the elite allele of Xpsp3152 frequently co-segregated with the larger grain haplotype of TaGW2-6A, suggesting probable genetic and functional linkages between Xpsp3152 and GW2 that are important for grain weight control in cereal plants. Our study provides new knowledge on TGW control in elite common wheat lines, which may aid the improvement of wheat grain weight trait in further research.
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Affiliation(s)
- Kunpu Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Junjun Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Liyi Zhang
- Guizhou Institute of Upland Crops, Guiyang, China
| | - Chaowu Rong
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fengwu Zhao
- Dry-Land Farming Institute, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
| | - Tao Peng
- Jiyuan Institute of Agricultural Sciences, Jiyuan, China
| | - Huimin Li
- Dry-Land Farming Institute, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
| | - Dongmei Cheng
- Jiyuan Institute of Agricultural Sciences, Jiyuan, China
| | - Xin Liu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Huanju Qin
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Aimin Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yiping Tong
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Daowen Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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144
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Bordes J, Ravel C, Jaubertie JP, Duperrier B, Gardet O, Heumez E, Pissavy AL, Charmet G, Le Gouis J, Balfourier F. Genomic regions associated with the nitrogen limitation response revealed in a global wheat core collection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:805-822. [PMID: 23192671 DOI: 10.1007/s00122-012-2019-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 11/05/2012] [Indexed: 05/27/2023]
Abstract
Modern wheat (Triticum aestivum L.) varieties in Western Europe have mainly been bred, and selected in conditions where high levels of nitrogen-rich fertilizer are applied. However, high input crop management has greatly increased the risk of nitrates leaching into groundwater with negative impacts on the environment. To investigate wheat nitrogen tolerance characteristics that could be adapted to low input crop management, we supplied 196 accessions of a wheat core collection of old and modern cultivars with high or moderate amounts of nitrogen fertilizer in an experimental network consisting of three sites and 2 years. The main breeding traits were assessed including grain yield and grain protein content. The response to nitrogen level was estimated for grain yield and grain number per m(2) using both the difference and the ratio between performance at the two input levels and the slope of joint regression. A large variability was observed for all the traits studied and the response to nitrogen level. Whole genome association mapping was carried out using 899 molecular markers taking into account the five ancestral group structure of the collection. We identified 54 main regions involving almost all chromosomes that influence yield and its components, plant height, heading date and grain protein concentration. Twenty-three regions, including several genes, spread over 16 chromosomes were involved in the response to nitrogen level. These chromosomal regions may be good candidates to be used in breeding programs to improve the performance of wheat varieties at moderate nitrogen input levels.
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Affiliation(s)
- Jacques Bordes
- INRA, UMR 1095 Génétique, Diversité Et Ecophysiologie Des Céréales, 234 Avenue Du Brézet, 63100, Clermont-Ferrand, France.
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145
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Bonneau J, Taylor J, Parent B, Bennett D, Reynolds M, Feuillet C, Langridge P, Mather D. Multi-environment analysis and improved mapping of a yield-related QTL on chromosome 3B of wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:747-61. [PMID: 23262551 DOI: 10.1007/s00122-012-2015-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 11/01/2012] [Indexed: 05/18/2023]
Abstract
Improved mapping, multi-environment quantitative trait loci (QTL) analysis and dissection of allelic effects were used to define a QTL associated with grain yield, thousand grain weight and early vigour on chromosome 3BL of bread wheat (Triticum aestivum L.) under abiotic stresses. The QTL had pleiotropic effects and showed QTL x environment interactions across 21 diverse environments in Australia and Mexico. The occurrence and the severity of water deficit combined with high temperatures during the growing season affected the responsiveness of this QTL, resulting in a reversal in the direction of allelic effects. The influence of this QTL can be substantial, with the allele from one parent (RAC875) increasing grain yield by up to 12.5 % (particularly in environments where both heat and drought stress occurred) and the allele from the other parent (Kukri) increasing grain yield by up to 9 % in favourable environments. With the application of additional markers and the genotyping of additional recombinant inbred lines, the genetic map in the QTL region was refined to provide a basis for future positional cloning.
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Affiliation(s)
- Julien Bonneau
- Australian Centre for Plant Functional Genomics and School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia.
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146
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Li B, Choulet F, Heng Y, Hao W, Paux E, Liu Z, Yue W, Jin W, Feuillet C, Zhang X. Wheat centromeric retrotransposons: the new ones take a major role in centromeric structure. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:952-65. [PMID: 23253213 DOI: 10.1111/tpj.12086] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 11/22/2012] [Accepted: 11/27/2012] [Indexed: 05/21/2023]
Abstract
The physical map of the hexaploid wheat chromosome 3B was screened using centromeric DNA probes. A 1.1-Mb region showing the highest number of positive bacterial artificial chromosome (BAC) clones was fully sequenced and annotated, revealing that 96% of the DNA consisted of transposable elements, mainly long terminal repeat (LTR) retrotransposons (88%). Estimation of the insertion time of the transposable elements revealed that CRW (also called Cereba) and Quinta are the youngest elements at the centromeres of common wheat (Triticum spp.) and its diploid ancestors, with Quinta being younger than CRW in both diploid and hexaploid wheats. Chromatin immunoprecipitation experiments revealed that both CRW and Quinta families are targeted by the centromere-specific histone H3 variant CENH3. Immuno colocalization of retroelements and CENH3 antibody indicated that a higher proportion of Quinta than CRWs was associated with CENH3, although CRWs were more abundant. Long arrays of satellite repeats were also identified in the wheat centromere regions, but they lost the ability to bind with CENH3. In addition to transposons, two functional genes and one pseudogene were identified. The gene density in the centromere appeared to be between three and four times lower than the average gene density of chromosome 3B. Comparisons with related grasses also indicated a loss of microcollinearity in this region. Finally, comparison of centromeric sequences of Aegilops tauschii (DD), Triticum boeoticum (AA) and hexaploid wheat revealed that the centromeres in both the polyploids and diploids are still undergoing dynamic changes, and that the new CRWs and Quintas may have undertaken the core role in kinetochore formation.
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Affiliation(s)
- Baochun Li
- Key Laboratory of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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147
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Investigation on series of length of coding and non-coding DNA sequences of bacteria using multifractal detrended cross-correlation analysis. J Theor Biol 2013; 321:54-62. [DOI: 10.1016/j.jtbi.2012.12.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 12/27/2012] [Accepted: 12/31/2012] [Indexed: 11/22/2022]
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148
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Giorgi D, Farina A, Grosso V, Gennaro A, Ceoloni C, Lucretti S. FISHIS: fluorescence in situ hybridization in suspension and chromosome flow sorting made easy. PLoS One 2013; 8:e57994. [PMID: 23469124 PMCID: PMC3585268 DOI: 10.1371/journal.pone.0057994] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 01/29/2013] [Indexed: 11/23/2022] Open
Abstract
The large size and complex polyploid nature of many genomes has often hampered genomics development, as is the case for several plants of high agronomic value. Isolating single chromosomes or chromosome arms via flow sorting offers a clue to resolve such complexity by focusing sequencing to a discrete and self-consistent part of the whole genome. The occurrence of sufficient differences in the size and or base-pair composition of the individual chromosomes, which is uncommon in plants, is critical for the success of flow sorting. We overcome this limitation by developing a robust method for labeling isolated chromosomes, named Fluorescent In situ Hybridization In suspension (FISHIS). FISHIS employs fluorescently labeled synthetic repetitive DNA probes, which are hybridized, in a wash-less procedure, to chromosomes in suspension following DNA alkaline denaturation. All typical A, B and D genomes of wheat, as well as individual chromosomes from pasta (T. durum L.) and bread (T. aestivum L.) wheat, were flow-sorted, after FISHIS, at high purity. For the first time in eukaryotes, each individual chromosome of a diploid organism, Dasypyrum villosum (L.) Candargy, was flow-sorted regardless of its size or base-pair related content. FISHIS-based chromosome sorting is a powerful and innovative flow cytogenetic tool which can develop new genomic resources from each plant species, where microsatellite DNA probes are available and high quality chromosome suspensions could be produced. The joining of FISHIS labeling and flow sorting with the Next Generation Sequencing methodology will enforce genomics for more species, and by this mightier chromosome approach it will be possible to increase our knowledge about structure, evolution and function of plant genome to be used for crop improvement. It is also anticipated that this technique could contribute to analyze and sort animal chromosomes with peculiar cytogenetic abnormalities, such as copy number variations or cytogenetic aberrations.
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Affiliation(s)
- Debora Giorgi
- ENEA – Italian National Agency for New Technologies, Energy and Sustainable Economic Development, CASACCIA Research Center, Rome, Italy
| | - Anna Farina
- ENEA – Italian National Agency for New Technologies, Energy and Sustainable Economic Development, CASACCIA Research Center, Rome, Italy
| | - Valentina Grosso
- ENEA – Italian National Agency for New Technologies, Energy and Sustainable Economic Development, CASACCIA Research Center, Rome, Italy
| | - Andrea Gennaro
- DAFNE – Department of Agriculture, Forestry, Nature and Energy, University of Tuscia, Viterbo, Italy
| | - Carla Ceoloni
- DAFNE – Department of Agriculture, Forestry, Nature and Energy, University of Tuscia, Viterbo, Italy
| | - Sergio Lucretti
- ENEA – Italian National Agency for New Technologies, Energy and Sustainable Economic Development, CASACCIA Research Center, Rome, Italy
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149
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Hastie AR, Dong L, Smith A, Finklestein J, Lam ET, Huo N, Cao H, Kwok PY, Deal KR, Dvorak J, Luo MC, Gu Y, Xiao M. Rapid genome mapping in nanochannel arrays for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome. PLoS One 2013; 8:e55864. [PMID: 23405223 PMCID: PMC3566107 DOI: 10.1371/journal.pone.0055864] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 01/03/2013] [Indexed: 02/04/2023] Open
Abstract
Next-generation sequencing (NGS) technologies have enabled high-throughput and low-cost generation of sequence data; however, de novo genome assembly remains a great challenge, particularly for large genomes. NGS short reads are often insufficient to create large contigs that span repeat sequences and to facilitate unambiguous assembly. Plant genomes are notorious for containing high quantities of repetitive elements, which combined with huge genome sizes, makes accurate assembly of these large and complex genomes intractable thus far. Using two-color genome mapping of tiling bacterial artificial chromosomes (BAC) clones on nanochannel arrays, we completed high-confidence assembly of a 2.1-Mb, highly repetitive region in the large and complex genome of Aegilops tauschii, the D-genome donor of hexaploid wheat (Triticum aestivum). Genome mapping is based on direct visualization of sequence motifs on single DNA molecules hundreds of kilobases in length. With the genome map as a scaffold, we anchored unplaced sequence contigs, validated the initial draft assembly, and resolved instances of misassembly, some involving contigs <2 kb long, to dramatically improve the assembly from 75% to 95% complete.
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Affiliation(s)
- Alex R. Hastie
- BioNano Genomics, San Diego, California, United States of America
| | - Lingli Dong
- Genomics and Gene Discovery Research Unit, United States Department of Agriculture - Agricultural Research Service, Albany, California, United States of America
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Alexis Smith
- BioNano Genomics, San Diego, California, United States of America
| | - Jeff Finklestein
- BioNano Genomics, San Diego, California, United States of America
| | - Ernest T. Lam
- BioNano Genomics, San Diego, California, United States of America
| | - Naxin Huo
- Genomics and Gene Discovery Research Unit, United States Department of Agriculture - Agricultural Research Service, Albany, California, United States of America
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Han Cao
- BioNano Genomics, San Diego, California, United States of America
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Karin R. Deal
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Jan Dvorak
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Yong Gu
- Genomics and Gene Discovery Research Unit, United States Department of Agriculture - Agricultural Research Service, Albany, California, United States of America
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
- * E-mail: (MX); (YG)
| | - Ming Xiao
- BioNano Genomics, San Diego, California, United States of America
- * E-mail: (MX); (YG)
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150
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Edwards D, Batley J, Snowdon RJ. Accessing complex crop genomes with next-generation sequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1-11. [PMID: 22948437 DOI: 10.1007/s00122-012-1964-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 08/08/2012] [Indexed: 05/02/2023]
Abstract
Many important crop species have genomes originating from ancestral or recent polyploidisation events. Multiple homoeologous gene copies, chromosomal rearrangements and amplification of repetitive DNA within large and complex crop genomes can considerably complicate genome analysis and gene discovery by conventional, forward genetics approaches. On the other hand, ongoing technological advances in molecular genetics and genomics today offer unprecedented opportunities to analyse and access even more recalcitrant genomes. In this review, we describe next-generation sequencing and data analysis techniques that vastly improve our ability to dissect and mine genomes for causal genes underlying key traits and allelic variation of interest to breeders. We focus primarily on wheat and oilseed rape, two leading examples of major polyploid crop genomes whose size or complexity present different, significant challenges. In both cases, the latest DNA sequencing technologies, applied using quite different approaches, have enabled considerable progress towards unravelling the respective genomes. Our ability to discover the extent and distribution of genetic diversity in crop gene pools, and its relationship to yield and quality-related traits, is swiftly gathering momentum as DNA sequencing and the bioinformatic tools to deal with growing quantities of genomic data continue to develop. In the coming decade, genomic and transcriptomic sequencing, discovery and high-throughput screening of single nucleotide polymorphisms, presence-absence variations and other structural chromosomal variants in diverse germplasm collections will give detailed insight into the origins, domestication and available trait-relevant variation of polyploid crops, in the process facilitating novel approaches and possibilities for genomics-assisted breeding.
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Affiliation(s)
- David Edwards
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD 4072, Australia
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